Theory of prokaryotic genome evolution

Significance Bacteria and archaea have small genomes with tightly packed protein-coding genes. Typically, this genome architecture is explained by “genome streamlining” (minimization) under selection for high replication rate. We developed a mathematical model of microbial evolution and tested it against extensive data from multiple genome comparisons to identify the key evolutionary forces. The results indicate that genome evolution is not governed by streamlining but rather, reflects the balance between the benefit of additional genes that diminishes with the genome size and the intrinsic preference for DNA deletion over acquisition. These results explain the observation that, in an apparent contradiction with the population genetic theory, microbes with large genomes reach higher abundance and are subject to stronger selection than small “streamlined” genomes.